[Dock-fans] SPHGEN problem

Michael Accardi Michael.Accardi at uoit.ca
Fri May 21 12:29:13 PDT 2010

To whom this may concern,

I recently installed DOCK 6.4. Unfortunately, when trying to dock a molecule into my protein I cannot get past the sphgen step. I have installed DOCK twice now, and I installed devel when I first installed cygwin.  I have looked through the archives and although some people have had a similar problem, no resolutions have worked for my situation.

Unlike in the dock 6 tutorial, I cannot simply write sphgen to start the program. When I do I receive this:
bash: sphgen: command not found

Instead, in order to get sphgen to 'work' I have to insert the following command:
run sphgen

After sphgen I am supposed to get 2 output files (the OUTSPH and a .sph file). However,  I only get a OUTSPH file which has nothing in it and a sphgen.exe.stackdump file but NO .sph file.

The sphgen.exe.stackdump contains the following:

Stack trace:
Frame     Function  Args
0023C3B8  7C802542  (000006C0, 0000EA60, 000000A4, 0023C4AC)
0023C4C8  610C2643  (00000000, 7C802600, 7C802542, 00000000)
0023C5A8  610BF2F7  (00000000, 00000000, 00000000, 00000000)
0023C5F8  610BF70B  (0000A9C8, 0023C620, FFFFFFDE, 00000006)
0023C6B8  610BF831  (0000A9C8, 00000006, 0023C6E8, 610BF8D5)
0023C6C8  610BF86C  (00000006, 0023CE80, 0023C6E8, 01A4CA18)
0023C6E8  610BF8D5  (00000006, 00000000, 00415C40, 00000000)
0023C708  004106EF  (00415C40, 00000001, 01A4C338, 00000190)
0023C858  0040A4AF  (00414080, 0023CC90, 00000050, 00000000)
0023CCF8  004010B1  (00405890, 01D019D0, 0023CD28, 004046A8)
0023CD28  004046D3  (00000001, 01D019D0, 01CD80E0, 00008000)
0023CD98  61006E73  (00000000, 0023CDD4, 61006720, 7FFDB000)
End of stack trace

Additionally in my INSPH file, which is not a .txt file, I have ensured that the name of my .dms file (which I generated with Chimera's Write DMS tool) is the same as the .dms file I placed in the same folder which contains the sphgen.exe (This location is in my dock6/bin folder). Therefore, the sphgen.exe, INSPH and .dms file are located in the same folder.

Do you have any help or advice?

Thanks in advance,

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